NSA2012 Short reads and Oyster Genome Resources

Short-read sequencing used forgenomic characterization inaquacultured shellfishSteven RobertsUniversity of WashingtonSchool of Aquatic and Fishery Sciences

e growth disease resistance color stress tolerance Traits

e growth disease resistance color stress tolerance e Traits m to rip c nsTra

e growth disease resistance color Traits m m Epigenetics

Outline Disease tolerance [Mercenaria mercenaria] Environmental response [Ostrea lurida] Epigenenetics [Crassostrea gigas]

Disease toleranceQPX and Mercenaria mercenaria

Broodstock : Broodstock :survived disease naive to disease pressure pressure BARN MASH

Broodstock : Broodstock :survived disease naive to disease pressure pressure BARN MASH 1 year Ken Hammond

Broodstock : Broodstock :survived disease naive to disease pressure pressure BARN MASH 12% QPX Prevalence 45% QPX Prevalence Ken Hammond

RNA-Seq Ken Hammond100 million reads 8482 contigs

RNA-Seq Ken Hammond 684 DEGs 459 higher inBARN (superior)

RNA-Seq 684 DEGs 459 higher inBARN (superior) 33 enriched biological processes

Ken Hammond 684 DEGs 459 higher inBARN (superior) 33 enriched biological processes

apoptosis baculoviral IAP repeat-containing protein, apoptosis 1 inhibitor, TNF receptor- associated factor 3, protein FADD adhesion 684 DEGs neuroglian, protocadherin oxidation reduction processes 459 higher in peroxidasin, thyroid peroxidase, epidermis-type lipoxygenase,BARN (superior) hydroxysteroid 11-beta-dehydrogenase, 33 enriched carbonyl reductase, cytochrome P450, superoxide dismutase, sorbitol biological dehydrogenase processes translation asparaginyl-tRNA synthetase, eukaryotic initiation factor, tryptophanyl-tRNA synthetase, eukaryotic peptide chain release factor subunit

Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction EnzymeAssistedDigestion-Sequencing

Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction Enzyme Reduce RepresentationAssistedDigestion-Sequencing

Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction Enzyme Reduce RepresentationAssistedDigestion-Sequencing Sequence multiple individuals

Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction Enzyme Reduce RepresentationAssistedDigestion-Sequencing Sequence multiple individuals 145 Diagnostic Markers

Environmental stressOcean acidification and oyster larvaeOstrea lurida

Environmental stressOcean acidification and oyster larvaeOstrea lurida 400 million reads de novo assembly

Environmental stressOcean acidification and oyster larvaeOstrea lurida 400 million reads de novo assembly RNA-Seq 9605 DEGs 7474 annotated 4345 processes

Environmental stressOcean acidification and oyster larvaeOstrea lurida 400 million reads de novo assembly RNA-Seq 9605 DEGs 7474 annotated 4345 processes 55 enriched processes

Environmental stressOcean acidification and oyster larvaeOstrea lurida 400 million reads de novo assembly RNA-Seq Can provide information on physiological impact that 9605 DEGs might not be directly evident. 7474 annotated 4345 processes 55 enriched processes

EpigeneticsDNA methylation in Crassostrea gigas

EpigeneticsDNA methylation in Crassostrea gigas www.tokresource.org

EpigeneticsMBD-Seq genomic DNA fragment MBD Y MBD Y enrich MBD Y sequence

Epigenetics High resolution mapping efforts Coupling Bisulfite Sequencing with MBD MBD Y MBD Y MBD Y

Epigenetics - directions Are epigenetic marks independent of genetics marks? What role do epigenetic marks play in commercially important traits? What are the mechanisms of action of DNA methylation marks?

Genomic Resourcesfor Crassostrea gigas Essential for epigenetic analysis and valuable for other efforts.

Genomic Resourcesfor Crassostrea gigas

Genomic Resourcesfor Crassostrea gigas Tracks

Genomic Resourcesfor Crassostrea gigas Tracks (ﬁles) can be viewed in a variety of software. most are free

Genomic Resourcesfor Crassostrea gigas Developing simple portal (JBrowse)

Genomic Resourcesfor Crassostrea gigas Galaxy - is an open, web-based platform for data intensive biomedical research.

Genomic Resourcesfor Crassostrea gigas •Methylation •alternative splicing •mutation •transient methylation •relationship with gene expression

Genomic Resourcesfor Crassostrea gigas •Gene Discovery •Methylation •qPCR design •alternative •RNA-Seq splicing •mutation •RAD-Seq •transient •Gene Structure methylation •Genetic Diversity •relationship with gene expression •Phylogenetics •more...

SummaryLimited, ultra-short read sequencing canefficiently provide relevant biologicalinformation and genomic resources.

SummaryLimited, ultra-short read sequencing canefficiently provide relevant biologicalinformation and genomic resources.Availability of shared transcriptomic andgenomic sequences will facilitate increasedapplication of short-read sequencingtechnology.

Acknowledgements fundingScott Lindell USDADave Bushek NRACJohn KraeuterCaroline Storer NOAA Saltonstall-Kennedy Washington Sea GrantCarolyn Friedman EPA UWDave Metzger STARSam White more informationMackenzie Gavery fish.washington.edu/genefish

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NSA2012 Short reads and Oyster Genome Resources

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